Polymer nanostructures composed of poly(3-dodecylthiophene) (PDDT) have been directly written with control of polymer strand alignment and monolayer-by-monolayer thickness down to a single molecular monolayer (2.6 nm). The molecularly ordered nanostructures were written on silicon oxide surfaces using thermal dip-pen nanolithography, where an atomic force microscope cantilever with integrated tip heater was precoated with solid PDDT. The PDDT was precisely deposited onto the surface when the tip temperature was set close to PDDT's melting temperature.